8ASN | pdb_00008asn

Crystal structure of the apo human TTL in complex with tubulin-stathmin

PDB DOI: https://doi.org/10.2210/pdb8ASN/pdb

Classification: CELL CYCLE
Organism(s): Bos taurus, Rattus norvegicus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-19 Released: 2022-09-21
Deposition Author(s): Vuillard, L., Miallau, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.273 (Depositor), 0.260 (DCC)
R-Value Work:
0.243 (Depositor), 0.230 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the apo human TTL in complex with tubulin-stathmin

Vuillard, L., Miallau, L.

To be published.

Macromolecule Content

Total Structure Weight: 397.28 kDa
Atom Count: 26,206
Modeled Residue Count: 3,178
Deposited Residue Count: 3,467
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Bos taurus	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947 Go to UniProtKB: P81947
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6B856
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	143	Rattus norvegicus	Mutation(s): 0 Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043 Go to UniProtKB: P63043
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin--tyrosine ligase	F, G, H, I	383	Homo sapiens	Mutation(s): 0 Gene Names: TTL EC: 6.3.2.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NG68 (Homo sapiens) Explore Q8NG68 Go to UniProtKB: Q8NG68
PHAROS: Q8NG68 GTEx: ENSG00000114999
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NG68
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth C] MOL2 format, chain K [auth A] MOL2 format, chain P [auth C] mmCIF format, chain K [auth A] mmCIF format, chain P [auth C]	K [auth A], P [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain K [auth A] Focus chain P [auth C] Interactions & Density Focus chain K [auth A] Focus chain P [auth C]
ACP (Subject of Investigation/LOI) Query on ACP Download Ideal Coordinates CCD File SDF format, chain U [auth I] SDF format, chain T [auth H] SDF format, chain S [auth G] SDF format, chain R [auth F] MOL2 format, chain U [auth I] MOL2 format, chain T [auth H] MOL2 format, chain S [auth G] MOL2 format, chain R [auth F] mmCIF format, chain U [auth I] mmCIF format, chain T [auth H] mmCIF format, chain S [auth G] mmCIF format, chain R [auth F]	R [auth F], S [auth G], T [auth H], U [auth I]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Interactions & Density Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I]
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain L [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain L [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain L [auth B]	L [auth B], Q [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain L [auth B] Focus chain Q [auth D] Interactions & Density Focus chain L [auth B] Focus chain Q [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C]	J [auth A], M [auth B], N [auth B], O [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C]